Climate change induced drying and flooding may alter the redox conditions of organic matter decomposition in peat soils. The seasonal and intermittent changes in pore water solutes (NO₃⁻, Fe²⁺, SO₄²⁻, H₂S, acetate) and dissolved soil gases (CO₂, O₂, CH₄, H₂) under natural water table fluctuations were compared to the response under a reinforced drying and flooding in fen peats. Oxygen penetration during dryings led to CO₂ and CH₄ degassing and to a regeneration of dissolved electron acceptors (NO₃⁻, Fe³⁺ and SO₄²⁻). Drying intensity controlled the extent of the electron acceptor regeneration. Iron was rapidly reduced and sulfate pools ~ 1 mM depleted upon rewetting and CH₄ did not substantially accumulate until sulfate levels declined to ~ 100 μmol L⁻¹. The post-rewetting recovery of soil methane concentrations to levels ~ 80 μmol L⁻¹ needed 40–50 days after natural drought. This recovery was prolonged after experimentally reinforced drought. A greater regeneration of electron acceptors during drying was not related to prolonged methanogenesis suppression after rewetting. Peat compaction, solid phase content of reactive iron and total reduced inorganic sulfur and organic matter content controlled oxygen penetration, the regeneration of electron acceptors and the recovery of CH₄ production, respectively. Methane production was maintained despite moderate water table decline of 20 cm in denser peats. Flooding led to accumulation of acetate and H₂, promoted CH₄ production and strengthened the co-occurrence of iron and sulfate reduction and methanogenesis. Mass balances during drying and flooding indicated that an important fraction of the electron flow must have been used for the generation and consumption of electron acceptors in the solid phase or other mechanisms. In contrast to flooding, dry-wet cycles negatively affect methane production on a seasonal scale, but this impact might strongly depend on drying intensity and on the peat matrix, of which structure and physical properties influence moisture content.

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